Figure 4.

Sample-specific lincRNA expression. A, Comparison of the number of samples showing expression of coding and noncoding genes. Expression of noncoding genes is more sample specific. B, Number of total and unique lincRNA genes expressed in each tissue (samples from different time points for the same tissue were combined). Tissues with the highest total number of lincRNAs expressed and the highest number of uniquely expressed lincRNAs are floral tissue and shoot apical meristem. C, Number of lincRNAs expressed in each sample. The sample with most lincRNAs expressed is flower 1. D, Heat map showing relationships between samples. Samples from the same tissue have similar lincRNA expression profiles and cluster together. The color corresponds to distance calculated as 1-cor(log1p(FPKM)). Clustering was performed using hclust, method = complete. E, Tau expression specificity index calculated for lincRNA loci and three groups of protein coding genes representing different biological processes. Higher values of Tau correspond to more sample specific expression. Cotyledon 1, germination stage; cotyledon 2, trefoil stage; flower 1, flower bud differentiation stage; flower 2, flowering stage, bud before flowering; flower 3, flowering stage, florescence; flower 4, flowering stage, 5 d after flowering; flower 5, flowering stage, florescence, different stage; leaf 1, trefoil stage; leaf 2, flower bud differentiation stage; leaf 3, senescent leaves; leaf bud 1, germination stage; leaf bud 2, trefoil stage; leaf bud 3, flower bud differentiation stage; pod seed 1, 2 weeks; pod seed 2, 3 weeks; pod seed 3, 4 weeks; pod 1, 3 weeks; pod 2, 4 weeks; pod 3, 5 weeks; seed 1, 3 weeks; seed 2, 5 weeks; seed 3, 6 weeks; seed 4, 8 weeks; seed 5, 10 weeks; shoot meristem, flower bud differentiation stage; stem 1, germination; stem 2, trefoil stage; root, germination stage; sam sd0, SAM before short-day treatment; sam sd1-4, SAM short days 1 to 4; leaf sd0, leaf before short-day treatment; leaf sd1-3, leaf short days 1 to 3.